4U0B: Hexamer HIV-1 CA

Hexamer HIV-1 CA in complex with CPSF6 peptide, P212121 crystal form. Determined by X-ray diffraction at 2.8 Å resolution. Released 12 Nov 2014.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Human immunodeficiency virus type 1 group M subtype B, Homo sapiens
Chains: 24
Atoms: 19,958
Mol. weight: 324.14 kDa
Released: 12 Nov 2014

Explore 4U0B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4U0B contains 181 α-helices and 24 β-strands across 24 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	11-12	2	1
α-helix	14-16	3
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-57	9
α-helix	63-83	21
α-helix	101-104	4
α-helix	111-119	9
α-helix	126-145	20
α-helix	150-152	3
α-helix	161-175	15
α-helix	179-184	6
α-helix	185-189	5
α-helix	190-192	3
α-helix	196-205	10
α-helix	211-217	7

Chain B: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	2
β-strand	11-12	2	2
α-helix	14-16	3
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-57	9
α-helix	63-83	21
α-helix	97-99	3
α-helix	101-105	5
α-helix	111-118	8
α-helix	126-145	20
α-helix	150-152	3
α-helix	161-175	15
α-helix	189-192	4
α-helix	196-203	8
α-helix	211-217	7

Chain C: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	3
β-strand	11-12	2	3
α-helix	14-16	3
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-57	9
α-helix	63-83	21
α-helix	101-105	5
α-helix	111-118	8
α-helix	126-145	20
α-helix	150-152	3
α-helix	161-175	15
α-helix	189-192	4
α-helix	196-205	10
α-helix	211-217	7

Chain D: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	4
β-strand	11-12	2	4
α-helix	14-16	3
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-57	9
α-helix	63-83	21
α-helix	97-99	3
α-helix	101-105	5
α-helix	111-118	8
α-helix	126-145	20
α-helix	150-152	3
α-helix	161-175	15
α-helix	189-192	4
α-helix	196-205	10
α-helix	211-217	7

Chains E, G and K: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	5
β-strand	11-12	2	5
α-helix	14-16	3
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-57	9
α-helix	63-83	21
α-helix	101-105	5
α-helix	111-118	8
α-helix	126-145	20
α-helix	150-152	3
α-helix	161-175	15
α-helix	187-192	6
α-helix	196-205	10
α-helix	211-217	7

Chain F: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	6
β-strand	11-12	2	6
α-helix	14-16	3
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-57	9
α-helix	63-83	21
α-helix	101-105	5
α-helix	111-118	8
α-helix	126-145	20
α-helix	150-152	3
α-helix	161-175	15
α-helix	179-184	6
α-helix	185-189	5
α-helix	190-192	3
α-helix	196-205	10
α-helix	211-217	7

Chain H: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	8
β-strand	11-12	2	8
α-helix	14-16	3
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-57	9
α-helix	63-83	21
α-helix	101-105	5
α-helix	111-118	8
α-helix	126-145	20
α-helix	150-152	3
α-helix	161-175	15
α-helix	184-192	9
α-helix	196-205	10
α-helix	211-217	7

Chain I: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	9
β-strand	11-12	2	9
α-helix	14-16	3
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-57	9
α-helix	63-83	21
α-helix	90-92	3
α-helix	97-99	3
α-helix	101-105	5
α-helix	111-118	8
α-helix	126-145	20
α-helix	150-152	3
α-helix	161-175	15
α-helix	187-192	6
α-helix	196-205	10
α-helix	211-217	7

7 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein p24	A, B, C, D, E, F, G, H, I, J, K, L	protein	231	Human immunodeficiency virus type 1 group M subtype B	P12493
Cleavage and polyadenylation specificity factor subunit 6	M, N, O, P, Q, R, S, T, U, V, W, X	protein	15	Homo sapiens	Q16630 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L), FASTA

>4U0B_1 Capsid protein p24 (chains A, B, C, D, E, F, G, H, I, J, K, L)
PIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTVG
GHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTH
NPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQE
VKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL

Sequence of entity 2 (M, N, O, P, Q, R, S, T, U, V, W, X), FASTA

>4U0B_2 Cleavage and polyadenylation specificity factor subunit 6 (chains M, N, O, P, Q, R, S, T, U, V, W, X)
PVLFPGQPFGQPPLG

Primary citation

Host Cofactors and Pharmacologic Ligands Share an Essential Interface in HIV-1 Capsid That Is Lost upon Disassembly. Price, A.J., Jacques, D.A., McEwan, W.A. et al. PLoS Pathog (2014) 10:e1004459-e1004459. DOI 10.1371/journal.ppat.1004459 · PubMed

Other PDB entries of the same protein (UniProt P12493), best resolution first:

8QUK 1.38 Å, Hexameric HIV-1 CA in complex with DDD00100439
8QUH 1.55 Å, Hexameric HIV-1 CA in complex with DDD00057456
8FIU 1.56 Å, Potent long-acting inhibitors targeting HIV-1 capsid based on a versatile…
8QUB 1.63 Å, Hexameric HIV-1 CA in complex with DDD00074110
8QUJ 1.63 Å, Hexameric HIV-1 CA in complex with DDD00100452
8QUL 1.67 Å, Hexameric HIV-1 CA in complex with DDD00100555
8QUI 1.69 Å, Hexameric HIV-1 CA in complex with DDD00024969
5JPA 1.7 Å, Hexameric HIV-1 CA H12Y mutant
8QV9 1.76 Å, Hexameric HIV-1 CA in complex with DDD01829021
4U0C 1.77 Å, Hexameric HIV-1 CA in complex with Nup153 peptide, P6 crystal form
8VRP 1.8 Å, HIV-CA Disulfide linked Hexamer bound to 4-Quinazolinone Scaffold inhibitor
8QUY 1.88 Å, Hexameric HIV-1 CA in complex with DDD01728501

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